Condensing Raman spectrum for single-cell phenotype analysis
文献类型：期刊论文
| 作者 | Ning,Kang1,3,4; Bu,Dongbo5; Su,Xiaoquan4; Ren,Lihui4; Gao,Xin2; Wang,Xuetao3,4; Sun,Shiwei5 |
| 刊名 | BMC Bioinformatics
 |
| 出版日期 | 2015-12-09 |
| 卷号 | 16期号:Suppl 18 |
| ISSN号 | 1471-2105 |
| 关键词 | Raman Spectrum Linear Discriminant Analysis (LDA) K Nearest Neighbor(k-NN) Discretization |
| DOI | 10.1186/1471-2105-16-S18-S15 |
| 英文摘要 | AbstractBackgroundIn recent years, high throughput and non-invasive Raman spectrometry technique has matured as an effective approach to identification of individual cells by species, even in complex, mixed populations. Raman profiling is an appealing optical microscopic method to achieve this. To fully utilize Raman proling for single-cell analysis, an extensive understanding of Raman spectra is necessary to answer questions such as which filtering methodologies are effective for pre-processing of Raman spectra, what strains can be distinguished by Raman spectra, and what features serve best as Raman-based biomarkers for single-cells, etc.ResultsIn this work, we have proposed an approach called rDisc to discretize the original Raman spectrum into only a few (usually less than 20) representative peaks (Raman shifts). The approach has advantages in removing noises, and condensing the original spectrum. In particular, effective signal processing procedures were designed to eliminate noise, utilising wavelet transform denoising, baseline correction, and signal normalization. In the discretizing process, representative peaks were selected to signicantly decrease the Raman data size. More importantly, the selected peaks are chosen as suitable to serve as key biological markers to differentiate species and other cellular features. Additionally, the classication performance of discretized spectra was found to be comparable to full spectrum having more than 1000 Raman shifts. Overall, the discretized spectrum needs about 5storage space of a full spectrum and the processing speed is considerably faster. This makes rDisc clearly superior to other methods for single-cell classication. |
| 语种 | 英语 |
| 出版者 | BioMed Central |
| WOS记录号 | BMC:10.1186/1471-2105-16-S18-S15 |
| 源URL | [http://119.78.100.204/handle/2XEOYT63/4104]  |
| 专题 | 中国科学院计算技术研究所期刊论文_英文 |
| 通讯作者 | Ning,Kang; Bu,Dongbo |
| 作者单位 | 1.Huazhong University of Science and Technology; College of Life Science and Technology 2.King Abdullah University of Science and Technology; Computational Bioscience Research Center 3.CUDA Research Centre of Qingdao 4.Bioinformatics Group of Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences; CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics 5.Institute of Computing Technology of the Chinese Academy of Sciences; Key Lab of Intelligent Information Processing |
| 推荐引用方式 GB/T 7714 | Ning,Kang,Bu,Dongbo,Su,Xiaoquan,et al. Condensing Raman spectrum for single-cell phenotype analysis[J]. BMC Bioinformatics,2015,16(Suppl 18). |
| APA | Ning,Kang.,Bu,Dongbo.,Su,Xiaoquan.,Ren,Lihui.,Gao,Xin.,...&Sun,Shiwei.(2015).Condensing Raman spectrum for single-cell phenotype analysis.BMC Bioinformatics,16(Suppl 18). |
| MLA | Ning,Kang,et al."Condensing Raman spectrum for single-cell phenotype analysis".BMC Bioinformatics 16.Suppl 18(2015). |
入库方式： OAI收割
来源：计算技术研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。